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Protocol Buffers - Google's data interchange format
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Suspecting multiple protobuf in my Ubuntu PC causing "undefined reference" issues while compiling #4001

Closed ravijo closed 6 years ago

ravijo commented 6 years ago

Hi, I am trying to use protobuf inside ROS Indigo in my Ubuntu 14.04 LTS PC. Every time, when I compile the project, I am getting undefined reference issues. Below is the snippet of errors:

Linking CXX executable /home/ravi/ros_ws/devel/lib/protobuf_ros_tutorial/add_person
CMakeFiles/add_person.dir/src/add_person.cc.o: In function `PromptForAddress(tutorial::Person*)':
add_person.cc:(.text+0x6a): undefined reference to `google::protobuf::internal::fixed_address_empty_string'
add_person.cc:(.text+0x1a5): undefined reference to `google::protobuf::internal::ArenaImpl::AllocateAlignedAndAddCleanup(unsigned long, void (*)(void*))'
add_person.cc:(.text+0x1cc): undefined reference to `google::protobuf::internal::fixed_address_empty_string'

Initially, I installed protobuf from source but it went wrong and then I decided to use apt-get. apt-get installed protobuf 2.*. I knew that it is a blunder mistake and hence I treid to removed protobuf. Well, after this, I installed protobuf latest from GitHub source. I realized that protoc --version is working well and but still getting "undefined reference" issues.

I tried to search installed protobuf on my Ubuntu PC and found multiple entries. Please see below:

apt list output:

ravi@lab:~/ros_ws$ apt list --installed|grep protoc

WARNING: apt does not have a stable CLI interface yet. Use with caution in scripts.

liblwp-protocol-https-perl/trusty-updates,trusty-security,now 6.04-2ubuntu0.1 all [installed,automatic]
libprotoc8/trusty,now 2.5.0-9ubuntu1 amd64 [installed,automatic]
libunity-protocol-private0/trusty,now 7.1.4+14.04.20140210-0ubuntu1 amd64 [installed]

dpkg -l output:

ravi@lab:~/ros_ws$ dpkg -l |grep protoc
ii  apturl                                                0.5.2ubuntu4                                        amd64        install packages using the apt protocol - GTK+ frontend
ii  apturl-common                                         0.5.2ubuntu4                                        amd64        install packages using the apt protocol - common data
ii  empathy                                               3.8.6-0ubuntu9.2                                    amd64        GNOME multi-protocol chat and call client
ii  empathy-common                                        3.8.6-0ubuntu9.2                                    all          GNOME multi-protocol chat and call client (common files)
ii  libcmis-0.4-4                                         0.4.1-3ubuntu4                                      amd64        CMIS protocol client library
ii  libdbusmenu-qt2:amd64                                 0.9.3+14.04.20140314-0ubuntu1                       amd64        Qt implementation of the DBusMenu protocol
ii  libdbusmenu-qt5:amd64                                 0.9.3+14.04.20140314-0ubuntu1                       amd64        Qt5 implementation of the DBusMenu protocol
ii  libijs-0.35                                           0.35-8build1                                        amd64        IJS raster image transport protocol: shared library
ii  liblwp-protocol-https-perl                            6.04-2ubuntu0.1                                     all          HTTPS driver for LWP::UserAgent
ii  libmbim-glib0:amd64                                   1.6.0-2ubuntu0.1                                    amd64        Support library to use the MBIM protocol
ii  libmeanwhile1                                         1.0.2-4.1ubuntu1                                    amd64        open implementation of the Lotus Sametime Community Client protocol
ii  libmms0:amd64                                         0.6.2-3ubuntu2.1                                    amd64        MMS stream protocol library - shared library
ii  libopenobex1                                          1.5-2.1                                             amd64        OBEX protocol library
ii  libprotobuf-dev:amd64                                 2.5.0-9ubuntu1                                      amd64        protocol buffers C++ library (development files)
ii  libprotobuf-lite8:amd64                               2.5.0-9ubuntu1                                      amd64        protocol buffers C++ library (lite version)
ii  libprotobuf8:amd64                                    2.5.0-9ubuntu1                                      amd64        protocol buffers C++ library
ii  libprotoc8:amd64                                      2.5.0-9ubuntu1                                      amd64        protocol buffers compiler library
ii  libpurple-bin                                         1:2.10.9-0ubuntu3.4                                 all          multi-protocol instant messaging library - extra utilities
ii  libpurple0                                            1:2.10.9-0ubuntu3.4                                 amd64        multi-protocol instant messaging library
ii  libqmi-glib0:amd64                                    1.4.0-1                                             amd64        Support library to use the Qualcomm MSM Interface (QMI) protocol
ii  libspice-server1:amd64                                0.12.4-0nocelt2ubuntu1.5                            amd64        Implements the server side of the SPICE protocol
ii  libunity-protocol-private0:amd64                      7.1.4+14.04.20140210-0ubuntu1                       amd64        binding to get places into the launcher - private library
ii  libxkbcommon-x11-0:amd64                              0.4.1-0ubuntu1                                      amd64        library to create keymaps with the XKB X11 protocol
ii  mcp-account-manager-uoa                               3.8.6-0ubuntu9.2                                    amd64        GNOME multi-protocol chat and call client (UOA plugin)
ii  nautilus-sendto-empathy                               3.8.6-0ubuntu9.2                                    amd64        GNOME multi-protocol chat and call client (nautilus-sendto plugin)
ii  protobuf-compiler                                     2.5.0-9ubuntu1                                      amd64        compiler for protocol buffer definition files
ii  python-crypto                                         2.6.1-4ubuntu0.2                                    amd64        cryptographic algorithms and protocols for Python
ii  python-oauth                                          1.0.1-3build2                                       all          Python library implementing of the OAuth protocol
ii  python-twisted-web                                    13.2.0-1ubuntu1                                     all          HTTP protocol implementation together with clients and servers
ii  python-urlgrabber                                     3.9.1-4ubuntu3.14.04.1                              all          A high-level cross-protocol url-grabber
ii  python3-crypto                                        2.6.1-4ubuntu0.2                                    amd64        cryptographic algorithms and protocols for Python 3
ii  ros-indigo-xmlrpcpp                                   1.11.21-0trusty-20170312-161337-0700                amd64        XmlRpc++ is a C++ implementation of the XML-RPC protocol.
ii  x11proto-composite-dev                                1:0.4.2-2                                           all          X11 Composite extension wire protocol
ii  x11proto-core-dev                                     7.0.26-1~ubuntu2                                    all          X11 core wire protocol and auxiliary headers
ii  x11proto-damage-dev                                   1:1.2.1-2                                           all          X11 Damage extension wire protocol
ii  x11proto-dri2-dev                                     2.8-2                                               all          X11 DRI2 extension wire protocol
ii  x11proto-fixes-dev                                    1:5.0-2ubuntu2                                      all          X11 Fixes extension wire protocol
ii  x11proto-gl-dev                                       1.4.17-1                                            all          X11 OpenGL extension wire protocol
ii  x11proto-input-dev                                    2.3-1                                               all          X11 Input extension wire protocol
ii  x11proto-kb-dev                                       1.0.6-2                                             all          X11 XKB extension wire protocol
ii  x11proto-randr-dev                                    1.5.0-1~trusty2                                     all          X11 RandR extension wire protocol
ii  x11proto-render-dev                                   2:0.11.1-2                                          all          X11 Render extension wire protocol
ii  x11proto-scrnsaver-dev                                1.2.2-1                                             all          X11 Screen Saver extension wire protocol
ii  x11proto-xext-dev                                     7.3.0-1                                             all          X11 various extension wire protocol
ii  x11proto-xf86vidmode-dev                              2.3.1-2                                             all          X11 Video Mode extension wire protocol
ii  x11proto-xinerama-dev                                 1.2.1-2                                             all          X11 Xinerama extension wire protocol

What's going wrong here? Any workaround, please?

Thank you very much.

acozzette commented 6 years ago

It looks to me like there is a mismatch between your protoc version and the version of the protobuf library that you're linking against. To simplify things it might help to remove protobuf-compiler and libprotobuf*, since that way you would only be working with protoc and libraries built from source.

ravijo commented 6 years ago

Thanks a lot. I removed protobuf-compiler using sudo apt-get purge --remove protobuf-compiler command. However, when I tried to remove libprotobuf* I found that it may remove some of the ROS packages. Please see below:

ravi@lab:~/ros_ws$ sudo apt-get purge --remove libprotobuf*
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Note, selecting 'libprotobuf-dev' for regex 'libprotobuf*'
Note, selecting 'libprotobuf8' for regex 'libprotobuf*'
Note, selecting 'libprotobuf-c0-dev' for regex 'libprotobuf*'
Note, selecting 'libprotobuf-c0' for regex 'libprotobuf*'
Note, selecting 'libprotobuf-java' for regex 'libprotobuf*'
Note, selecting 'libprotobuf-lite8' for regex 'libprotobuf*'
Package 'libprotobuf-c0' is not installed, so not removed
Package 'libprotobuf-c0-dev' is not installed, so not removed
Package 'libprotobuf-java' is not installed, so not removed
The following packages were automatically installed and are no longer required:
  collada-dom-dev collada-dom2.4-dp-base collada-dom2.4-dp-dev hddtemp
  liballegro4.4 liballegro4.4-plugin-alsa libcegui-mk2-0.7.6 libcegui-mk2-dev
  libdevil-dev libdevil1c2 libfltk1.1 libfltk1.1-dev libgeos-3.4.2 libgeos-c1
  libgnomecanvas2-0 libgnomecanvas2-common libgsl0ldbl liblcms1 liblcms1-dev
  liblcms2-dev liblodo3.0 liblua5.1-0-dev libmng-dev libois-1.3.0
  libplayerc++3.0 libplayerc3.0 libplayercommon3.0 libplayercore3.0
  libplayerdrivers3.0 libplayerinterface3.0 libplayerjpeg3.0 libplayertcp3.0
  libplayerwkb3.0 libpmap3.0 libreadline-dev libreadline6-dev libsdformat-dev
  libsdformat1 libsilly libstatgrab9 libtar0 libtbb-dev libtinfo-dev
  liburdfdom-tools liburiparser1 python-opengl python-psutil python-pydot
  robot-player ros-indigo-actionlib-tutorials ros-indigo-bond-core
  ros-indigo-camera-calibration ros-indigo-collada-parser
  ros-indigo-collada-urdf ros-indigo-common-msgs ros-indigo-common-tutorials
  ros-indigo-compressed-depth-image-transport
  ros-indigo-compressed-image-transport ros-indigo-desktop
  ros-indigo-diagnostic-analysis ros-indigo-diagnostic-common-diagnostics
  ros-indigo-diagnostics ros-indigo-executive-smach ros-indigo-filters
  ros-indigo-gazebo-msgs ros-indigo-geometry ros-indigo-geometry-tutorials
  ros-indigo-gl-dependency ros-indigo-image-common ros-indigo-image-pipeline
  ros-indigo-image-rotate ros-indigo-image-transport-plugins
  ros-indigo-image-view ros-indigo-interactive-marker-tutorials
  ros-indigo-joint-state-publisher ros-indigo-laser-assembler
  ros-indigo-laser-filters ros-indigo-laser-pipeline
  ros-indigo-librviz-tutorial ros-indigo-mk ros-indigo-nodelet-core
  ros-indigo-nodelet-tutorial-math ros-indigo-perception
  ros-indigo-perception-pcl ros-indigo-pluginlib-tutorials
  ros-indigo-pointcloud-to-laserscan ros-indigo-polled-camera
  ros-indigo-qt-dotgraph ros-indigo-qt-gui-cpp ros-indigo-robot
  ros-indigo-robot-model ros-indigo-robot-state-publisher ros-indigo-ros
  ros-indigo-ros-base ros-indigo-ros-comm ros-indigo-ros-core
  ros-indigo-ros-tutorials ros-indigo-rosbash ros-indigo-rosboost-cfg
  ros-indigo-roscpp-core ros-indigo-roscpp-tutorials ros-indigo-roscreate
  ros-indigo-roslang ros-indigo-roslint ros-indigo-roslisp ros-indigo-rosmake
  ros-indigo-rqt-action ros-indigo-rqt-bag ros-indigo-rqt-bag-plugins
  ros-indigo-rqt-common-plugins ros-indigo-rqt-console ros-indigo-rqt-dep
  ros-indigo-rqt-graph ros-indigo-rqt-gui-cpp ros-indigo-rqt-image-view
  ros-indigo-rqt-launch ros-indigo-rqt-logger-level ros-indigo-rqt-moveit
  ros-indigo-rqt-msg ros-indigo-rqt-nav-view ros-indigo-rqt-pose-view
  ros-indigo-rqt-publisher ros-indigo-rqt-py-console
  ros-indigo-rqt-reconfigure ros-indigo-rqt-robot-dashboard
  ros-indigo-rqt-robot-monitor ros-indigo-rqt-robot-plugins
  ros-indigo-rqt-robot-steering ros-indigo-rqt-runtime-monitor
  ros-indigo-rqt-rviz ros-indigo-rqt-service-caller ros-indigo-rqt-shell
  ros-indigo-rqt-srv ros-indigo-rqt-tf-tree ros-indigo-rqt-top
  ros-indigo-rqt-topic ros-indigo-rqt-web ros-indigo-rviz-plugin-tutorials
  ros-indigo-rviz-python-tutorial ros-indigo-smach ros-indigo-smach-msgs
  ros-indigo-smach-ros ros-indigo-stage ros-indigo-stage-ros
  ros-indigo-stereo-image-proc ros-indigo-stereo-msgs
  ros-indigo-tf2-geometry-msgs ros-indigo-tf2-kdl ros-indigo-tf2-sensor-msgs
  ros-indigo-theora-image-transport ros-indigo-turtle-actionlib
  ros-indigo-turtle-tf ros-indigo-turtle-tf2 ros-indigo-turtlesim
  ros-indigo-urdf-tutorial ros-indigo-vision-opencv
  ros-indigo-visualization-marker-tutorials ros-indigo-visualization-tutorials
  ros-indigo-viz sbcl
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
  compiz* compiz-gnome* gazebo2* libcompizconfig0* libprotobuf-dev*
  libprotobuf-lite8* libprotobuf8* libprotoc8* ros-indigo-desktop-full*
  ros-indigo-gazebo-plugins* ros-indigo-gazebo-ros*
  ros-indigo-gazebo-ros-control* ros-indigo-gazebo-ros-pkgs*
  ros-indigo-simulators* unity*
0 upgraded, 0 newly installed, 15 to remove and 151 not upgraded.
After this operation, 87.5 MB disk space will be freed.
Do you want to continue? [Y/n]

The above seems too dangerous to proceed. What do you say? Meanwhile, I am thinking, If protocol buffer is already installed by ROS Indigo, instead of installing new protobuf, is there any way to use the existing protobuf?

acozzette commented 6 years ago

Sure, you could use the existing protobuf installed via apt. In that case you would want to reinstall protobuf-compiler so that you have protoc available. The main downside, though, is that the version of protobuf currently shipped with Ubuntu is 2.5, which is pretty old at this point. If you do this then you might also want to verify that you don't have a built-from-source protobuf library somewhere in /usr/local where it might take preference over the version installed with apt-get.

ravijo commented 6 years ago

I reinstalled protobuf-compiler and now I have libprotoc 2.5.0. Please see below:

ravi@lab:~/ros_ws$ protoc --version
libprotoc 2.5.0
ravi@lab:~/ros_ws$ whereis protoc
protoc: /usr/bin/protoc /usr/bin/X11/protoc /usr/share/man/man1/protoc.1.gz

I still suspect that some other versions are also existing. sudo apt-get purge --remove libprotobuf* is showing the same as above (in the beginning of this post).

Although, I tried to search, but I am not sure how to proceed in this situation. Please see below:

ravi@lab:/usr/local$ find /usr/local -name libprotoc*
ravi@lab:/usr/local$ find /usr/local -name protoc*
/usr/local/lib/python2.7/dist-packages/prompt_toolkit/contrib/telnet/protocol.pyc
/usr/local/lib/python2.7/dist-packages/prompt_toolkit/contrib/telnet/protocol.py
/usr/local/texlive/2017/tlpkg/tlpobj/protocol.tlpobj
/usr/local/texlive/2017/texmf-dist/doc/latex/protocol
/usr/local/texlive/2017/texmf-dist/doc/latex/protocol/protocol.pdf
/usr/local/texlive/2017/texmf-dist/source/latex/protocol
/usr/local/texlive/2017/texmf-dist/source/latex/protocol/protocol.dtx
/usr/local/texlive/2017/texmf-dist/source/latex/protocol/protocol.ins
/usr/local/texlive/2017/texmf-dist/tex/latex/protocol
/usr/local/texlive/2017/texmf-dist/tex/latex/protocol/protocol.cls

Please suggest some workaround.

ravijo commented 6 years ago

Hi, I would like to add my findings in order to make the debugging simpler. Today morning, I installed a ROS Indigo on fresh Ubuntu 14.04 LTS VM. Then I installed protobuf-compilerusing sudo apt-get protobuf-compiler. Now I have libprotoc 2.5.0, which is fine.

After this, I just compiled my project and it compiled without any issues. I believe that in my original PC, other versions of protocol buffers are existing. How to remove them without disturbing ROS?

acozzette commented 6 years ago

The package manager will not generally put anything in /usr/local, so removing protobuf libraries and headers from /usr/local should not affect your ROS packages. I believe you would want to remove the headers in /usr/local/include/google/protobuf and libraries beginning with libprotoc and libprotobuf in /usr/local/lib.

ravijo commented 6 years ago

Surprisingly, these files do not exist. Please see below:

ravi@lab:~$ ls -la /usr/local/include/google/protobuf
ls: cannot access /usr/local/include/google/protobuf: No such file or directory
ravi@lab:/usr/local/include$ ls -la
total 8
drwxr-xr-x  2 root root 4096 Apr 17  2014 .
drwxr-xr-x 11 root root 4096 Feb  8  2017 ..
ravi@lab:/usr/local/include$ cd /usr/local/lib
ravi@lab:/usr/local/lib$ ls
perl  python2.7  python3.4
ravi@lab:/usr/local/lib$ find . -name libprotoc*
ravi@lab:/usr/local/lib$ find . -name libprotobuf*
acozzette commented 6 years ago

@ravijo If those files don't exist then it seems to me like you should be good to go, with just one protobuf version installed on your system--are you still running into any problems?

ravijo commented 6 years ago

Yes. I am getting the same errors (posted in the top of this thread)

Linking CXX executable /home/ravi/ros_ws/devel/lib/protobuf_ros_tutorial/add_person
CMakeFiles/add_person.dir/src/add_person.cc.o: In function `PromptForAddress(tutorial::Person*)':
add_person.cc:(.text+0x6a): undefined reference to `google::protobuf::internal::fixed_address_empty_string'

By the way, I have another idea in my mind. Can you help me to implement it? Inside a ROS pacakage sub directory, I extracted protobuf-3.5.0. In this way cmake files are located in lib/protobuf-3.5.0/cmake. The ROS Package contains CMakeLists.txt which is complied using catkin_make.

I want to know that how to configure my ROS Package CMakeLists.txt so that it uses locally installed Protocol Buffers (kept inside `lib/protobuf-3.5.0 location)?

acozzette commented 6 years ago

@ravijo I'm not familiar with ROS at all so it's hard for me to say how to make it work with your protobuf subdirectory. I'm guessing that something is wrong with your build setup. Is your tutorial code using a protoc other than /usr/bin/protoc?

ravijo commented 6 years ago

@acozzette: Basically the problem arrived since I installed protocol buffer 3 from source and I was unaware that the older version of protocol buffer is being used by ROS and already present in the system. Although, I followed your suggestion to remove the protocol buffer 3 but the problem still exists.

Below is the more information about protoc:

ravi@lab:~/ros_ws$ whereis protoc
protoc: /usr/bin/protoc /usr/bin/X11/protoc /usr/share/man/man1/protoc.1.gz
ravi@lab:~/ros_ws$ protoc --version
libprotoc 2.5.0

Well, I am in the process of debugging. I will get back to you once I finish it. Thanks again.

ravijo commented 6 years ago

I did following workaround to solve the issue:

I realized that I just need following two variables to compile and run with Protocol Buffers:

  1. Protobuf_INCLUDE_DIRS
  2. Protobuf_LIBRARIES

Hence, I added following lines in CMakeLists.txt:

set(PROTOBUF_FOLDER ${PROJECT_SOURCE_DIR}/lib/protobuf-3.5.0)

set(Protobuf_INCLUDE_DIRS ${PROTOBUF_FOLDER}/include)
set(Protobuf_LIBRARIES ${PROTOBUF_FOLDER}/lib/libprotobuf.so)

Please note that Protocol Buffers was installed locally by using ./configure --prefix=$PWD inside lib/protobuf-3.5.0 directory.

acozzette commented 6 years ago

Great, I'm glad you were able to find a solution.

JerryZsy commented 5 years ago

good partners

srediske commented 5 years ago

Hi, i guess i have a very similar problem. I'm trying to run an old example for a RL Algorithm in ROS/Gazebo and face some Problems with my protoc or protobuf version. I have to use conda and i'm not sure if this is part of the Problem.

Here is the Error output:

[libprotobuf FATAL google/protobuf/stubs/common.cc:67] This program requires version 3.5.0 of the Protocol Buffer runtime library, but the installed version is 3.0.0.  Please update your library.  If you compiled the program yourself, make sure that your headers are from the same version of Protocol Buffers as your link-time library.  (Version verification failed in "/tmp/build/80754af9/opencv-suite_1535558553474/work/modules/dnn/misc/caffe/opencv-caffe.pb.cc".)
terminate called after throwing an instance of 'google::protobuf::FatalException'
  what():  This program requires version 3.5.0 of the Protocol Buffer runtime library, but the installed version is 3.0.0.  Please update your library.  If you compiled the program yourself, make sure that your headers are from the same version of Protocol Buffers as your link-time library.  (Version verification failed in "/tmp/build/80754af9/opencv-suite_1535558553474/work/modules/dnn/misc/caffe/opencv-caffe.pb.cc".)
Aborted (core dumped)
[gazebo-4] process has died [pid 5734, exit code 134, cmd /home/stephan/catkin_ws/src/gazebo_ros_pkgs/gazebo_ros/scripts/gzserver -u -e ode /home/stephan/catkin_ws/src/ardupilot_sitl_gazebo_plugin/ardupilot_sitl_gazebo_plugin/worlds/empty_world/empty.world __name:=gazebo __log:=/home/stephan/.ros/log/a0633a2a-6b1e-11e9-88e0-50e54953a336/gazebo-4.log].
log file: /home/stephan/.ros/log/a0633a2a-6b1e-11e9-88e0-50e54953a336/gazebo-4*.log

apt-list output:

(cuda) stephan@stephan-Z:~$ apt list --installed|grep protoc

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

liblwp-protocol-https-perl/bionic,bionic,now 6.07-2 all [installed]
libprotoc-dev/bionic,now 3.0.0-9.1ubuntu1 amd64 [installed]
libprotoc10/bionic,now 3.0.0-9.1ubuntu1 amd64 [installed,automatic]
libunity-protocol-private0/bionic,now 7.1.4+18.04.20180209.1-0ubuntu2 amd64 [installed]
libx11-protocol-perl/bionic,bionic,now 0.56-7 all [installed]

dpkg -l output:

(cuda) stephan@stephan-Z:~$ dpkg -l |grep protoc
ii  apturl                                          0.5.2ubuntu14.2                              amd64        install packages using the apt protocol - GTK+ frontend
ii  apturl-common                                   0.5.2ubuntu14.2                              amd64        install packages using the apt protocol - common data
ii  libcmis-0.5-5v5                                 0.5.1+git20160603-3build2                    amd64        CMIS protocol client library
ii  libijs-0.35:amd64                               0.35-13                                      amd64        IJS raster image transport protocol: shared library
ii  liblwp-protocol-https-perl                      6.07-2                                       all          HTTPS driver for LWP::UserAgent
ii  libmbim-glib4:amd64                             1.14.2-2.1ubuntu1                            amd64        Support library to use the MBIM protocol
ii  libnghttp2-14:amd64                             1.30.0-1ubuntu1                              amd64        library implementing HTTP/2 protocol (shared library)
ii  libprotobuf-dev:amd64                           3.0.0-9.1ubuntu1                             amd64        protocol buffers C++ library (development files)
ii  libprotobuf-lite10:amd64                        3.0.0-9.1ubuntu1                             amd64        protocol buffers C++ library (lite version)
ii  libprotobuf10:amd64                             3.0.0-9.1ubuntu1                             amd64        protocol buffers C++ library
ii  libprotoc-dev:amd64                             3.0.0-9.1ubuntu1                             amd64        protocol buffers compiler library (development files)
ii  libprotoc10:amd64                               3.0.0-9.1ubuntu1                             amd64        protocol buffers compiler library
ii  libqmi-glib5:amd64                              1.18.0-3ubuntu1                              amd64        Support library to use the Qualcomm MSM Interface (QMI) protocol
ii  libunity-protocol-private0:amd64                7.1.4+18.04.20180209.1-0ubuntu2              amd64        binding to get places into the launcher - private library
ii  libx11-protocol-perl                            0.56-7                                       all          Perl module for the X Window System Protocol, version 11
ii  libxkbcommon-x11-0:amd64                        0.8.0-1ubuntu0.1                             amd64        library to create keymaps with the XKB X11 protocol
ii  protobuf-compiler                               3.0.0-9.1ubuntu1                             amd64        compiler for protocol buffer definition files
ii  python-crypto                                   2.6.1-8ubuntu2                               amd64        cryptographic algorithms and protocols for Python
ii  python-oauth                                    1.0.1-5                                      all          Python library implementing of the OAuth protocol
ii  python-pyasn1-modules                           0.2.1-0.2                                    all          Collection of protocols modules written in ASN.1 language
ii  python3-crypto                                  2.6.1-8ubuntu2                               amd64        cryptographic algorithms and protocols for Python 3
ii  python3-oauth                                   1.0.1-5                                      all          Python 3 library implementing of the OAuth protocol
ii  python3-protobuf                                3.0.0-9.1ubuntu1                             amd64        Python 3 bindings for protocol buffers
ii  ros-melodic-xmlrpcpp                            1.14.3-0bionic.20190318.180337               amd64        XmlRpc++ is a C++ implementation of the XML-RPC protocol.
ii  x11proto-dev                                    2018.4-4                                     all          X11 extension protocols and auxiliary headers

whereis output:

(cuda) stephan@stephan-Z:~$ whereis protoc
protoc: /usr/bin/protoc /home/stephan/miniconda2/envs/cuda/bin/protoc /usr/share/man/man1/protoc.1.gz
(cuda) stephan@stephan-Z:~$ whereis libprotobuf
libprotobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/libprotobuf.a

pip show output:

(cuda) stephan@stephan-Z:~$ pip show protobuf
Name: protobuf
Version: 3.7.1
Summary: Protocol Buffers
Home-page: https://developers.google.com/protocol-buffers/
Author: None
Author-email: None
License: 3-Clause BSD License
Location: /home/stephan/.local/lib/python2.7/site-packages
Requires: six, setuptools
Required-by: tensorflow-gpu, tensorboard

and at last my LD_LIBRARY_PATH, cause i read on other Threads that this may cause this error.

(cuda) stephan@stephan-Z:~$ $LD_LIBRARY_PATH 
bash: /home/stephan/catkin_ws/devel/lib:/home/stephan/gym-gazebo/gym_gazebo/envs/installation/catkin_ws/devel/lib:/opt/ros/melodic/lib:/usr/lib/x86_64-linux-gnu/gazebo-9/plugins: No such file or directory

For me it seems that i need libprotobuf 3.5.0 but the system has version 3.0.0 and only in my conda environment i have version 3.7.1, is that correct?

I used this command a few days ago to install libprotobuf: conda install -c anaconda libprotobuf

I' very grateful for any tips and help.